Subject: Support Open-Source! (was RE: Chime Encryption)

From: "DeLano, Warren" <[email-masked]>
Date: Sun, 16 Sep 2001 19:15:39 -0700

The Chime encryption issue is one more reason why we should support
open-source development in computational chemistry.  Hear me out...

What is going on is that both MDL and CamSoft recognize the utility (and
profit potential) for a tool which allows chemists to enter structures
onto a web page and then transfer them to a server.  The corresponding
function of retrieving structures from a database server and displaying
them in a web-page is also quite valuable.

Quite sensibly, both companies don't want their FREE plug-ins to have
this capacity, and their software license agreements may even prohibit
such usage.  They want you to pay for those valuable capabilities by
purchasing the professional plug-ins (or a corresponding
encryption-capable server-license).  Even though you can most-likely
defeat the protections in the FREE plug-ins, actually using them in this
manner would be illegal!

So how about nurturing a free and open-source alternative? 8->

Since plug-in support has been dropped from the latest version of
Internet Explorer, it is now clearly in the interest of both academia
and the pharmaceutical industry to FULLY SUPPORT development of a free
and open-source chemical ActiveX control capable of database interaction
> from a web-page.  

I believe that an ultra-light-weight 2D chemical display tool could be
developed in a couple of months by a competent programmer with
sufficient motivation.  This would obviate 90% of the need for ChimePro
and enable hundreds of new educational and industrial applications.  Who
will tackle this?  You would effectively be creating the "Linux kernel"
of chemical informatics!

Furthermore, based on my work with PyMOL http://www.pymol.org, I think
that an ActiveX/OpenGL based replacement for Chime's 3D rendering
capability can also be constructed quite rapidly and do far more than
Chime ever could.

Of couse, building a 2D drawing tool would be more difficult, but
JChemPaint http://jchempaint.sourceforge.net is already halfway there!
It just needs a few more features and some usability refinement to get
it ready for real-world settings.

The bottom line is that we need to motivate open-source developers by
coordinating support from industry and academia and by targeting
specific key functionalities.  The results will be well worth whatever
contributions are made because the overall return on investment will be
huge in light of how much we currently pay to MDL, Accelrys, etc.

Please drop me a short (one line!) email if you (or your organization)
might be interested in supporting such efforts OR if you are a developer
wishing to receive compensation for open-source programming.  I'd like
to start a discussion about how to best accomplish this and survey the
interest level on both sides.

Free/open-source software certainly won't replace most commercial
products, but competition from open-source in a few key areas will
greatly benefit the science by driving down the cost of commerical
products and at the same time increasing the quality of all available
software.  It is in YOUR INTEREST as a computational scientist to
support it! 

Cheers,
- Warren
--
mailto:[email-masked]
Warren L. DeLano, Ph.D.
Founder
DeLano Scientific
"Enabling New Science with 
 Advanced Open-Source Software"

> -----Original Message-----
> From: Jonathan Brecher [mailto:[email-masked]]
> Sent: Friday, September 14, 2001 1:38 PM
> To: jaouad
> Cc: [email-masked]
> Subject: CCL:Chime Encryption
> 
> 
> >I guess I did not explain very well the situation,
> >what I did is creating a web page where we use the
> >Chime plugin, so that permit us to call isis draw for
> >drawing of the structure we want and send it back to
> >the browser, now that we have the struture in our FORM
> >we submit it to the server by a Post format and try to
> >parse it, Here where the problem come, because when we
> >parse it we realize that the structure is encrypted
> >twice one by the server and that is normal and we can
> >deal with it, but the second encryption is Chime one
> >and we dont know how to solve that, i was wondering if
> >some one did found a solution to that.
> 
> Um... Did you try asking MDL?  Seems to me that if they're 
> encrypting their
> data, then maybe they don't *want* you decoding it...
> 
> We're doing something similar with the ChemDraw Plugin.  One 
> version of the
> ChemDraw Plugin produces encrypted data; one version produces 
> unencrypted
> data.
> 
> 
> Jonathan Brecher
> CambridgeSoft Corporation
> [email-masked]

---

From: Egon Willighagen <[email-masked]>
Date: Mon, 17 Sep 2001 08:21:39 +0200

> it ready for real-world settings.

Thanx for advertising JChemPaint on CCL! :)

Can you list the features and refinements you miss? I think most of the
JCP developers are interested in making JCP more usable. At least i am...
If you could state the missing stuff, we could see what we can add in the
next few weeks/months...

BTW, last year i gave a presentation in Washington,DC at ChemInt2000 about
a servlet for webservers for more intelligent publishing of chemical data.
A prototype is available, and later this year i am going to rewrite the
prototype to use CDK (http://cdk.sf.net/), on which JCP-2 is also based.
The prototype which i demonstrated on ChemInt 2000 can be downloaded from
CVS at http://sdwb.sf.net/ (GPL license).

To give a small outline of what the CDK based version will be able to do:
- publish structure databases:
  - JDBC based databases (e.g. MySQL)
  - directory structure based databases (MDL mol, CML, PDB, etc... formats)
- publication of XHTML documents containing CML fragments
- dynamically publish it in several formats depending on browser/platform
  - to develop ActiveX plugin for MS/IE
  - Chime-plugin for older MS/IE
  - Java-plugin for Netscape
  - GIF/PNG picture
  - etc
- user overwrite of this format
- support caching

Note that some of this stuff is already done by the first prototype.

Comments are welcomed.

Egon Willighagen